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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings Maaslin2_1.18.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
Maaslin2 89.672  1.187  90.805
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Maaslin2
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-05-31 05:08:28.174659 INFO::Writing function arguments to log file
2024-05-31 05:08:28.216607 INFO::Verifying options selected are valid
2024-05-31 05:08:28.254649 INFO::Determining format of input files
2024-05-31 05:08:28.256382 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-31 05:08:28.261623 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-31 05:08:28.263052 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2024-05-31 05:08:28.265648 INFO::Filter data based on min abundance and min prevalence
2024-05-31 05:08:28.266598 INFO::Total samples in data: 1595
2024-05-31 05:08:28.267491 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-31 05:08:28.27127 INFO::Total filtered features: 0
2024-05-31 05:08:28.272283 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-31 05:08:28.288403 INFO::Total filtered features with variance filtering: 0
2024-05-31 05:08:28.289683 INFO::Filtered feature names from variance filtering:
2024-05-31 05:08:28.290636 INFO::Running selected normalization method: TSS
2024-05-31 05:08:29.545932 INFO::Bypass z-score application to metadata
2024-05-31 05:08:29.547553 INFO::Running selected transform method: AST
2024-05-31 05:08:29.564774 INFO::Running selected analysis method: LM
2024-05-31 05:08:30.176974 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-31 05:08:30.560305 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-31 05:08:30.721365 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-31 05:08:30.875754 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-31 05:08:31.036708 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-31 05:08:31.18157 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-31 05:08:31.333744 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-31 05:08:31.484995 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-31 05:08:31.605691 WARNING::Fitting problem for feature 8 a warning was issued
2024-05-31 05:08:31.768088 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-31 05:08:31.890614 WARNING::Fitting problem for feature 9 a warning was issued
2024-05-31 05:08:32.072873 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-31 05:08:32.238901 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-31 05:08:32.391456 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-31 05:08:32.574007 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-31 05:08:32.704695 WARNING::Fitting problem for feature 13 a warning was issued
2024-05-31 05:08:32.87119 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-31 05:08:33.032935 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-31 05:08:33.212522 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-31 05:08:33.379785 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-31 05:08:33.545202 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-31 05:08:33.727487 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-31 05:08:33.876949 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-31 05:08:34.028803 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-31 05:08:34.188891 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-31 05:08:34.338012 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-31 05:08:34.495838 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-31 05:08:34.662735 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-31 05:08:34.830024 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-31 05:08:34.98796 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-31 05:08:35.151283 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-31 05:08:35.32157 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-31 05:08:35.474291 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-31 05:08:35.611214 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-31 05:08:35.767612 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-31 05:08:35.910054 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-31 05:08:36.076521 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-31 05:08:36.239509 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-31 05:08:36.395867 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-31 05:08:36.550152 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-31 05:08:36.724906 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-31 05:08:36.876268 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-31 05:08:37.033757 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-31 05:08:37.186224 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-31 05:08:37.331226 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-31 05:08:37.501683 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-31 05:08:37.660323 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-31 05:08:37.802577 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-31 05:08:37.958659 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-31 05:08:38.106909 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-31 05:08:38.265267 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-31 05:08:38.409176 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-31 05:08:38.556496 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-31 05:08:38.714224 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-31 05:08:38.857577 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-31 05:08:39.311911 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-31 05:08:39.487347 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-31 05:08:39.647509 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-31 05:08:39.835639 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-31 05:08:39.993341 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-31 05:08:40.133592 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-31 05:08:40.284379 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-31 05:08:40.42834 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-31 05:08:40.56451 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-31 05:08:40.710042 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-31 05:08:40.870542 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-31 05:08:41.01596 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-31 05:08:41.159296 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-31 05:08:41.309744 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-31 05:08:41.450316 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-31 05:08:41.585661 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-31 05:08:41.737107 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-31 05:08:41.885415 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-31 05:08:42.032933 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-31 05:08:42.199768 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-31 05:08:42.357452 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-31 05:08:42.537296 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-31 05:08:42.682414 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-31 05:08:42.840068 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-31 05:08:43.0058 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-31 05:08:43.158054 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-31 05:08:43.320856 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-31 05:08:43.477042 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-31 05:08:43.625693 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-31 05:08:43.783291 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-31 05:08:43.940396 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-31 05:08:44.091185 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-31 05:08:44.229168 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-31 05:08:44.370618 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-31 05:08:44.517812 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-31 05:08:44.70355 INFO::Counting total values for each feature
2024-05-31 05:08:44.745215 INFO::Writing filtered data to file output/features/filtered_data.tsv
2024-05-31 05:08:44.890765 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2024-05-31 05:08:45.042889 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2024-05-31 05:08:45.195798 INFO::Writing residuals to file output/fits/residuals.rds
2024-05-31 05:08:45.253703 INFO::Writing fitted values to file output/fits/fitted.rds
2024-05-31 05:08:45.286916 INFO::Writing extracted random effects to file output/fits/ranef.rds
2024-05-31 05:08:45.293071 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2024-05-31 05:08:45.300355 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2024-05-31 05:08:45.314906 INFO::Writing function arguments to log file
2024-05-31 05:08:45.321403 INFO::Verifying options selected are valid
2024-05-31 05:08:45.322461 INFO::Determining format of input files
2024-05-31 05:08:45.32361 INFO::Input format is data samples as rows and metadata samples as rows
2024-05-31 05:08:45.328624 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2024-05-31 05:08:45.329686 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2024-05-31 05:08:45.331283 INFO::Filter data based on min abundance and min prevalence
2024-05-31 05:08:45.332142 INFO::Total samples in data: 1595
2024-05-31 05:08:45.333035 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2024-05-31 05:08:45.337284 INFO::Total filtered features: 0
2024-05-31 05:08:45.338312 INFO::Filtered feature names from abundance and prevalence filtering:
2024-05-31 05:08:45.345768 INFO::Total filtered features with variance filtering: 0
2024-05-31 05:08:45.346804 INFO::Filtered feature names from variance filtering:
2024-05-31 05:08:45.347624 INFO::Running selected normalization method: NONE
2024-05-31 05:08:45.34847 INFO::Bypass z-score application to metadata
2024-05-31 05:08:45.349268 INFO::Running selected transform method: AST
2024-05-31 05:08:45.371207 INFO::Running selected analysis method: LM
2024-05-31 05:08:45.373609 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2024-05-31 05:08:45.538023 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2024-05-31 05:08:45.985144 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2024-05-31 05:08:46.124184 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2024-05-31 05:08:46.260966 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2024-05-31 05:08:46.401741 INFO::Fitting model to feature number 6, Bacteroides.caccae
2024-05-31 05:08:46.559222 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2024-05-31 05:08:46.695198 INFO::Fitting model to feature number 8, Bacteroides.dorei
2024-05-31 05:08:46.827034 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2024-05-31 05:08:46.970779 INFO::Fitting model to feature number 10, Bacteroides.faecis
2024-05-31 05:08:47.129796 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2024-05-31 05:08:47.254063 WARNING::Fitting problem for feature 11 a warning was issued
2024-05-31 05:08:47.401927 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2024-05-31 05:08:47.542377 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2024-05-31 05:08:47.698204 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2024-05-31 05:08:47.838574 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2024-05-31 05:08:47.989191 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2024-05-31 05:08:48.112909 WARNING::Fitting problem for feature 16 a warning was issued
2024-05-31 05:08:48.255921 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2024-05-31 05:08:48.398356 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2024-05-31 05:08:48.534394 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2024-05-31 05:08:48.668865 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2024-05-31 05:08:48.803655 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2024-05-31 05:08:48.93921 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2024-05-31 05:08:49.08814 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2024-05-31 05:08:49.218252 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2024-05-31 05:08:49.362387 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2024-05-31 05:08:49.509358 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2024-05-31 05:08:49.649323 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2024-05-31 05:08:49.816149 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2024-05-31 05:08:49.974764 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2024-05-31 05:08:50.117659 INFO::Fitting model to feature number 30, Paraprevotella.clara
2024-05-31 05:08:50.257866 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2024-05-31 05:08:50.405839 INFO::Fitting model to feature number 32, Prevotella.copri
2024-05-31 05:08:50.547448 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2024-05-31 05:08:50.684857 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2024-05-31 05:08:50.837002 INFO::Fitting model to feature number 35, Alistipes.putredinis
2024-05-31 05:08:50.969321 INFO::Fitting model to feature number 36, Alistipes.shahii
2024-05-31 05:08:51.116638 INFO::Fitting model to feature number 37, Alistipes.unclassified
2024-05-31 05:08:51.254397 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2024-05-31 05:08:51.391865 INFO::Fitting model to feature number 39, Clostridium.bolteae
2024-05-31 05:08:51.531791 INFO::Fitting model to feature number 40, Clostridium.citroniae
2024-05-31 05:08:51.671196 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2024-05-31 05:08:51.830336 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2024-05-31 05:08:51.973025 INFO::Fitting model to feature number 43, Clostridium.leptum
2024-05-31 05:08:52.110247 INFO::Fitting model to feature number 44, Clostridium.nexile
2024-05-31 05:08:52.260131 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2024-05-31 05:08:52.406931 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2024-05-31 05:08:52.570885 INFO::Fitting model to feature number 47, Eubacterium.eligens
2024-05-31 05:08:52.709832 INFO::Fitting model to feature number 48, Eubacterium.hallii
2024-05-31 05:08:53.123686 INFO::Fitting model to feature number 49, Eubacterium.rectale
2024-05-31 05:08:53.255609 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2024-05-31 05:08:53.37809 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2024-05-31 05:08:53.511764 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2024-05-31 05:08:53.643691 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2024-05-31 05:08:53.770063 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2024-05-31 05:08:53.901044 INFO::Fitting model to feature number 55, Ruminococcus.torques
2024-05-31 05:08:54.03947 INFO::Fitting model to feature number 56, Coprococcus.comes
2024-05-31 05:08:54.17155 INFO::Fitting model to feature number 57, Dorea.longicatena
2024-05-31 05:08:54.306951 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2024-05-31 05:08:54.445862 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2024-05-31 05:08:54.594954 INFO::Fitting model to feature number 60, Roseburia.hominis
2024-05-31 05:08:54.731782 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2024-05-31 05:08:54.870454 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2024-05-31 05:08:55.01813 INFO::Fitting model to feature number 63, Roseburia.unclassified
2024-05-31 05:08:55.154635 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2024-05-31 05:08:55.295322 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2024-05-31 05:08:55.469235 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2024-05-31 05:08:55.609454 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2024-05-31 05:08:55.730468 WARNING::Fitting problem for feature 67 a warning was issued
2024-05-31 05:08:55.891193 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2024-05-31 05:08:56.030555 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2024-05-31 05:08:56.176954 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2024-05-31 05:08:56.332491 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2024-05-31 05:08:56.479635 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2024-05-31 05:08:56.528137 WARNING::Fitting problem for feature 72 a warning was issued
2024-05-31 05:08:56.668349 INFO::Fitting model to feature number 73, Dialister.invisus
2024-05-31 05:08:56.81932 INFO::Fitting model to feature number 74, Veillonella.atypica
2024-05-31 05:08:56.955027 INFO::Fitting model to feature number 75, Veillonella.dispar
2024-05-31 05:08:57.08591 INFO::Fitting model to feature number 76, Veillonella.parvula
2024-05-31 05:08:57.22626 INFO::Fitting model to feature number 77, Veillonella.unclassified
2024-05-31 05:08:57.360447 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2024-05-31 05:08:57.501233 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2024-05-31 05:08:57.641205 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2024-05-31 05:08:57.773794 INFO::Fitting model to feature number 81, Bilophila.unclassified
2024-05-31 05:08:57.92314 INFO::Fitting model to feature number 82, Escherichia.coli
2024-05-31 05:08:58.057176 INFO::Fitting model to feature number 83, Escherichia.unclassified
2024-05-31 05:08:58.201158 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2024-05-31 05:08:58.331844 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2024-05-31 05:08:58.462748 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2024-05-31 05:08:58.605467 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2024-05-31 05:08:58.773722 INFO::Counting total values for each feature
2024-05-31 05:08:58.808883 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2024-05-31 05:08:58.954402 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2024-05-31 05:08:59.099102 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2024-05-31 05:08:59.251069 INFO::Writing residuals to file output2/fits/residuals.rds
2024-05-31 05:08:59.326071 INFO::Writing fitted values to file output2/fits/fitted.rds
2024-05-31 05:08:59.399442 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2024-05-31 05:08:59.405809 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2024-05-31 05:08:59.411902 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 31.703   0.748  32.442